Variant report

Variant	rs62024991
Chromosome Location	chr15:45005259-45005260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45002354-45013577	GM18951	blood:	n/a	n/a
2	PAX5	chr15:45004728-45005413	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:45002647-45005444	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
5	YY1	chr15:45004734-45005432	K562	blood:	n/a	n/a
6	POLR2A	chr15:45002339-45005459	K562	blood:	n/a	n/a
7	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
8	WRNIP1	chr15:45002331-45005445	GM12878	blood:	n/a	n/a
9	BCLAF1	chr15:45002272-45005506	GM12878	blood:	n/a	chr15:45003027-45003040 chr15:45003589-45003598 chr15:45003959-45003972 chr15:45003029-45003038 chr15:45005259-45005267 chr15:45003577-45003586 chr15:45004128-45004137
10	FOXM1	chr15:45002235-45005519	GM12878	blood:	n/a	n/a
11	PAX5	chr15:45004698-45005333	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:45002760-45005424	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
14	PAX5	chr15:45004938-45005286	GM12892	blood:	n/a	n/a
15	POLR2A	chr15:45003220-45005427	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
17	GATA1	chr15:45002260-45005291	PBDE	blood:	n/a	chr15:45002520-45002529
18	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
19	NR2F2	chr15:45003175-45005294	K562	blood:	n/a	n/a
20	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
21	BHLHE40	chr15:45002348-45005461	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:45002322-45013693	GM19193	blood:	n/a	n/a
23	POLR2A	chr15:45002218-45005514	HL-60	blood:	n/a	n/a
24	BCLAF1	chr15:45002327-45005451	GM12878	blood:	n/a	chr15:45003027-45003040 chr15:45003589-45003598 chr15:45003959-45003972 chr15:45003029-45003038 chr15:45005259-45005267 chr15:45003577-45003586 chr15:45004128-45004137
25	POLR2A	chr15:45002192-45013674	GM12891	blood:	n/a	n/a
26	UBTF	chr15:45004678-45005279	K562	blood:	n/a	n/a
27	RFX5	chr15:45001383-45006423	SK-N-SH	brain:	n/a	chr15:45003663-45003672
28	POLR2A	chr15:45002796-45006154	MCF10A-Er-Src	breast:	n/a	n/a
29	YY1	chr15:45004647-45005446	GM12892	blood:	n/a	n/a
30	MYC	chr15:45004700-45005300	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr15:45004273-45005329	MCF10A-Er-Src	breast:	n/a	n/a
32	SIN3A	chr15:45005063-45005425	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:45002251-45013700	GM19099	blood:	n/a	n/a
34	YY1	chr15:45004573-45005291	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:45002180-45010236	GM12892	blood:	n/a	n/a
36	MXI1	chr15:45002427-45005347	IMR90	lung:	n/a	n/a
37	YY1	chr15:45005012-45005295	A549	lung:	n/a	n/a
38	POLR2A	chr15:45002813-45005464	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:45002801-45006834	U87	brain:	n/a	n/a
40	NFIC	chr15:45001937-45005463	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:45002148-45013709	K562	blood:	n/a	n/a
42	CREB1	chr15:45003264-45005287	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:45003365-45006623	HepG2	liver:	n/a	n/a
44	POLR2A	chr15:45002113-45013784	GM12892	blood:	n/a	n/a
45	MTA3	chr15:45002069-45009622	GM12878	blood:	n/a	n/a
46	E2F4	chr15:45004229-45005394	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:45002407-45005437	K562	blood:	n/a	n/a
48	POLR2A	chr15:45003288-45005269	PANC-1	pancreas:	n/a	n/a
49	FOXM1	chr15:45002171-45005327	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:45002361-45005342	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:21112938..21114460-chr15:45004450..45006409,2	K562	blood:
2	chr15:45004559..45007244-chr15:45019568..45021417,3	MCF-7	breast:
3	chr15:44951739..44957508-chr15:45000588..45008057,33	K562	blood:
4	chr15:44980888..44990623-chr15:45002366..45006726,14	K562	blood:
5	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
6	chr15:44968315..44970113-chr15:45003699..45005679,2	MCF-7	breast:
7	chr15:44968819..44972092-chr15:45002551..45007992,5	K562	blood:
8	chr15:45000863..45005844-chr15:45018710..45023352,9	MCF-7	breast:
9	chr15:44951575..44958275-chr15:45001046..45006983,19	MCF-7	breast:
10	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

Variant related genes	Relation type
PATL2	TF binding region
B2M	TF binding region
ENSG00000127483	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000206957	Chromatin interaction
ENSG00000229474	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10163110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10444818	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1137516	0.81[EUR][1000 genomes]
rs11634059	0.81[EUR][1000 genomes]
rs11634063	0.81[EUR][1000 genomes]
rs11639157	0.81[EUR][1000 genomes]
rs12912870	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1630168	0.87[EUR][1000 genomes]
rs1669833	0.87[EUR][1000 genomes]
rs1690313	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16974543	0.87[EUR][1000 genomes]
rs1720723	0.87[EUR][1000 genomes]
rs1720724	0.87[EUR][1000 genomes]
rs1869125	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1901530	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1901538	0.81[EUR][1000 genomes]
rs2167595	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2468067	0.81[EUR][1000 genomes]
rs2470908	0.81[EUR][1000 genomes]
rs2960206	0.81[EUR][1000 genomes]
rs3100140	0.81[EUR][1000 genomes]
rs3100141	0.81[EUR][1000 genomes]
rs3110677	0.81[EUR][1000 genomes]
rs3759878	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3759881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923990	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4923991	0.81[EUR][1000 genomes]
rs4923993	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62025968	0.81[EUR][1000 genomes]
rs62025969	0.84[EUR][1000 genomes]
rs6416439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6416440	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493114	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493116	0.81[EUR][1000 genomes]
rs6493118	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493119	0.81[EUR][1000 genomes]
rs6493124	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493125	0.81[EUR][1000 genomes]
rs6493126	0.81[EUR][1000 genomes]
rs6493127	0.87[EUR][1000 genomes]
rs6493128	0.81[EUR][1000 genomes]
rs7151	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168090	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172357	0.81[EUR][1000 genomes]
rs7172376	0.81[EUR][1000 genomes]
rs7496437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7496559	0.87[EUR][1000 genomes]
rs7497862	0.85[AMR][1000 genomes]
rs8035787	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8036223	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8038532	0.84[EUR][1000 genomes]
rs935885	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs935888	0.81[EUR][1000 genomes]
rs935889	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45002000-45005600	Active TSS	Colon Smooth Muscle	Colon
2	chr15:45002000-45005800	Active TSS	Brain Anterior Caudate	brain
3	chr15:45002000-45006000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr15:45002200-45005800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:45002200-45006800	Active TSS	Colonic Mucosa	Colon
6	chr15:45002400-45005400	Active TSS	Brain Cingulate Gyrus	brain
7	chr15:45002400-45005400	Active TSS	Spleen	Spleen
8	chr15:45002400-45005600	Active TSS	Rectal Smooth Muscle	rectum
9	chr15:45002400-45005600	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr15:45002400-45006000	Active TSS	NHLF	lung
11	chr15:45002400-45006400	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr15:45002400-45006600	Active TSS	Lung	lung
13	chr15:45002400-45006600	Active TSS	Stomach Smooth Muscle	stomach
14	chr15:45002400-45006800	Active TSS	Small Intestine	intestine
15	chr15:45002400-45007000	Active TSS	Left Ventricle	heart
16	chr15:45002400-45007200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr15:45002400-45007200	Active TSS	Right Ventricle	heart
18	chr15:45002600-45005400	Active TSS	HSMM	muscle
19	chr15:45002600-45005600	Active TSS	NHEK	skin
20	chr15:45002600-45005800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:45002600-45005800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:45002600-45005800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr15:45002600-45006200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:45002600-45006200	Active TSS	Duodenum Mucosa	Duodenum
25	chr15:45002600-45006400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:45002600-45007200	Active TSS	Psoas Muscle	Psoas
27	chr15:45002800-45005400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:45002800-45005400	Active TSS	Aorta	Aorta
29	chr15:45002800-45005400	Active TSS	Brain Substantia Nigra	brain
30	chr15:45002800-45005400	Active TSS	Fetal Kidney	kidney
31	chr15:45002800-45005600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:45002800-45005600	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr15:45002800-45005600	Active TSS	Primary T cells from cord blood	blood
34	chr15:45002800-45005600	Active TSS	Fetal Thymus	thymus
35	chr15:45002800-45005600	Active TSS	Thymus	Thymus
36	chr15:45002800-45005600	Active TSS	A549	lung
37	chr15:45002800-45005800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr15:45002800-45005800	Active TSS	Brain Angular Gyrus	brain
39	chr15:45002800-45005800	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr15:45002800-45006000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:45002800-45006200	Active TSS	NHDF-Ad	bronchial
42	chr15:45002800-45006400	Active TSS	HSMMtube	muscle
43	chr15:45002800-45006600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:45002800-45006600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr15:45003000-45005400	Active TSS	Esophagus	oesophagus
46	chr15:45003000-45005400	Active TSS	Stomach Mucosa	stomach
47	chr15:45003000-45005600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:45003000-45005600	Active TSS	Liver	Liver
49	chr15:45003000-45005800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:45003000-45006000	Active TSS	Ovary	ovary

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